Genexus OPA Replicates

head(NGS_rep_long)

## # A tibble: 6 x 11
##   Sample Gene  AA    Var    Sample_Var Run      AF Mean_Sample_Var mean_minus_af
##   <chr>  <chr> <chr> <chr>  <chr>      <chr> <dbl>           <dbl>         <dbl>
## 1 2079   EGFR  R108K EGFR_~ 2079_EGFR~ 1st   0.052          0.0569      0.00486
## 2 2079   EGFR  R108K EGFR_~ 2079_EGFR~ 2nd   0.058          0.0569     -0.00114
## 3 2079   EGFR  R108K EGFR_~ 2079_EGFR~ 3rd   0.057          0.0569     -0.000143
## 4 2079   EGFR  R108K EGFR_~ 2079_EGFR~ 4th   0.052          0.0569      0.00486
## 5 2079   EGFR  R108K EGFR_~ 2079_EGFR~ 5th   0.06           0.0569     -0.00314
## 6 2079   EGFR  R108K EGFR_~ 2079_EGFR~ 5th   0.059          0.0569     -0.00214
## # ... with 2 more variables: abs_mean_minus_af <dbl>, percent_dif <dbl>

ALL SAMPLES

Run vs Alele Frequency

    p <- ggplot(data=NGS_rep_long, aes(Run, AF, group = Sample_Var, col = Sample_Var)) +
                  geom_point() +
                  geom_line() +
                  ggtitle("Run vs Allele Frequency: All Samples and Variants")

                ggplotly(p)

Run Vs. Difference

 p <- ggplot(data=NGS_rep_long, aes(Run, mean_minus_af, group = Sample_Var, col = Sample_Var)) +
                  geom_point() +
                  geom_line() +
                  geom_hline(yintercept = 0, linetype = "dashed", size = 0.2) +
                  ggtitle("Run vs (Mean AF - AF): All Samples and Variants") +
                  ylab("AF: Difference from Mean")

                ggplotly(p)

Run vs % Difference

% Difference = ((difference/mean) * 100)

p <- ggplot(data=NGS_rep_long, aes(Run, percent_dif, group = Sample_Var, col = Sample_Var)) +
                  geom_point() +
                  geom_line() +
                  geom_hline(yintercept = 0, linetype = "dashed", size = 0.2) +
                  ggtitle("Run vs Percent Difference ((AF/Mean AF)*100): All Samples and Variants") +
                  ylab("AF: Percent Difference")

                ggplotly(p)